setting:connect

Bonding

connect_bonded (boolean, default: off) controls whether or not bonds can be detected between atoms with explicit bonds in the PDB file.

connect_cutoff (float, default: 0.4) affects how close atoms need to be in order for bonds to be created.

connect_mode (integer, default: 0) controls how bonds are detected when PDB files are loaded.
- 0 = auto-connect and use explicit valences
- 1 = use explicit valences only
- 2 = reserved

half_bonds (boolean, default: off) controls whether or not half-bonds are shown when only one of the two atoms is visible.

hide_long_bonds (boolean, default: off) controls whether or not PyMOL hides bonds longer than 90% of the sum the vdw radii.

heavy_neighbor_cutoff (float, default: 3.5) boundary at which neighboring heavy atoms are no longer considered 'neighbors'.

trace_atoms_mode (integer 0-5, default: 0) affects how cartoon and ribbon traces are performed.

valence (boolean, default: off) controls whether or not bond valences are shown.

valence_size (float, default: 0.06) controls how far apart bond valences are drawn.

setting/connect.txt · Last modified: 2013/11/06 22:36 by vertrees